Abstract

The various schemes proposed to classify microorganisms in the living world have long been subject of heated debates. The classical dichotomic distinction between Prokaryotae (cells without nucleus) and Eukaryotae (cells with nucleus) functional and phenotypic categories was deeply changed by rRNA gene-based analysis that divided the living world into three phylogenetic domains: the Bacteria, the Archaea (originally Archaebacteria), and the Eukarya. In this chapter, we review the terms of this debate between the prokaryotic/eukaryotic functional and phenotypic dichotomy and the 16S/18S phylogenetic dichotomy that separates prokaryotes into two distinct domains. The specific characteristics that emphasize the organizational and functional complexity of prokaryotes and justify maintaining this terminology are discussed. We conclude that the organizational and functional concept of a prokaryotes/eukaryotes dichotomy can be easily supplemented by the phylogenetic concept Bacteria/Archaea/Eukarya. The two concepts are not irreconcilable but complementary, resulting in a consensual proposal that integrates both phenotypic and genotypic criteria.